5c8l: Difference between revisions

Latest revision as of 08:35, 27 September 2023

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase

Structural highlights

5c8l is a 2 chain structure with sequence from Bdellovibrio bacteriovorus HD100. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	GLC, GOL, PEG, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q6MIH8_BDEBA

Publication Abstract from PubMed

Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 A Calpha RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the alpha-beta-alpha NDPSase fold differentiates NDPSases from ADPRases.

Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.,de la Pena AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB PLoS One. 2015 Nov 2;10(11):e0141716. doi: 10.1371/journal.pone.0141716., eCollection 2015. PMID:26524597^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ de la Pena AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. PLoS One. 2015 Nov 2;10(11):e0141716. doi: 10.1371/journal.pone.0141716., eCollection 2015. PMID:26524597 doi:https://dx.doi.org/10.1371/journal.pone.0141716

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Pena AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. PLoS One. 2015 Nov 2;10(11):e0141716. doi: 10.1371/journal.pone.0141716., eCollection 2015. PMID:26524597 doi:https://dx.doi.org/10.1371/journal.pone.0141716

[1]

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase==
-<StructureSection load='5c8l' size='340' side='right' caption='[[5c8l]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='5c8l' size='340' side='right'caption='[[5c8l]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5c8l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C8L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C8L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5c8l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellovibrio_bacteriovorus_HD100 Bdellovibrio bacteriovorus HD100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C8L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c7q|5c7q]], [[5c7t|5c7t]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5c8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c8l OCA], [https://pdbe.org/5c8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c8l RCSB], [https://www.ebi.ac.uk/pdbsum/5c8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c8l ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5c8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c8l OCA], [http://pdbe.org/5c8l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c8l RCSB], [http://www.ebi.ac.uk/pdbsum/5c8l PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6MIH8_BDEBA Q6MIH8_BDEBA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: ADP-ribose diphosphatase]]
+[[Category: Bdellovibrio bacteriovorus HD100]]
-[[Category: Amzel, L M]]
+[[Category: Large Structures]]
-[[Category: Gabelli, S B]]
+[[Category: Amzel LM]]
-[[Category: Pena, A H.de la]]
+[[Category: Gabelli SB]]
-[[Category: Suarez, A]]
+[[Category: Suarez A]]
-[[Category: Hydrolase]]
+[[Category: De la Pena AH]]
-[[Category: Nudix]]

5c8l: Difference between revisions

Latest revision as of 08:35, 27 September 2023

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools